SLC22A3

solute carrier family 22 member 3, the group of Solute carrier family 22

Basic information

Region (hg38): 6:160348377-160452577

Links

ENSG00000146477 ∙ NCBI:6581 ∙ OMIM:604842 ∙ HGNC:10967 ∙ Uniprot:O75751 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC22A3 gene.

• Inborn genetic diseases (26 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC22A3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	1	2
missense			25	1		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	0	25	2	3

Variants in SLC22A3

This is a list of pathogenic ClinVar variants found in the SLC22A3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
6-160348391-G-A			Benign (Nov 14, 2019)
6-160348451-T-C		not specified	Likely benign (Apr 07, 2023)
6-160348535-T-C		not specified	Uncertain significance (Dec 19, 2023)
6-160348588-G-A		not specified	Uncertain significance (Apr 07, 2023)
6-160348600-G-C		not specified	Uncertain significance (Mar 27, 2023)
6-160348623-G-C		not specified	Uncertain significance (Sep 01, 2021)
6-160348651-T-C		not specified	Uncertain significance (Apr 07, 2023)
6-160348652-C-G		not specified	Uncertain significance (Apr 07, 2023)
6-160348655-G-T		not specified	Uncertain significance (Apr 07, 2023)
6-160348666-C-T		not specified	Uncertain significance (Aug 08, 2023)
6-160348677-C-G			Likely benign (Apr 10, 2018)
6-160348705-G-C		not specified	Uncertain significance (Jul 12, 2022)
6-160387116-C-T			Benign (Apr 30, 2020)
6-160397988-G-C		not specified	Uncertain significance (Mar 27, 2023)
6-160398006-A-C		not specified	Uncertain significance (Mar 07, 2024)
6-160407141-C-T		not specified	Uncertain significance (Jun 24, 2022)
6-160407157-T-A		not specified	Uncertain significance (Sep 26, 2022)
6-160407159-T-A		not specified	Uncertain significance (Jan 26, 2022)
6-160408771-C-T		not specified	Uncertain significance (Jan 23, 2024)
6-160408797-G-A		not specified	Uncertain significance (Dec 22, 2023)
6-160408839-G-A		not specified	Uncertain significance (Aug 22, 2023)
6-160408851-T-C		not specified	Uncertain significance (Apr 19, 2023)
6-160408861-A-G		not specified	Uncertain significance (Apr 07, 2022)
6-160408888-C-T		not specified	Uncertain significance (Dec 08, 2021)
6-160410763-C-T		not specified	Uncertain significance (Nov 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC22A3	protein_coding	protein_coding	ENST00000275300	11	106715

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.77e-10	0.695	125692	0	51	125743	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.485	279	303	0.922	0.0000166	3516
Missense in Polyphen		123	133.24	0.92317		1558
Synonymous	-0.359	126	121	1.04	0.00000675	1172
Loss of Function	1.42	18	25.8	0.697	0.00000130	286

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000293	0.000293
Ashkenazi Jewish	0.00	0.00
East Asian	0.000546	0.000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000123	0.000123
Middle Eastern	0.000546	0.000544
South Asian	0.000523	0.000523
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates potential-dependent transport of a variety of organic cations. May play a significant role in the disposition of cationic neurotoxins and neurotransmitters in the brain. {ECO:0000269|PubMed:10196521, ECO:0000269|PubMed:10966924}.
• Pathway: Choline metabolism in cancer - Homo sapiens (human);Lamivudine Pathway, Pharmacokinetics/Pharmacodynamics;Metformin Pathway, Pharmacokinetics;Sympathetic Nerve Pathway (Neuroeffector Junction);Lamivudine Metabolism Pathway;Synaptic Vesicle Pathway;Tyrosine metabolism;Abacavir transmembrane transport;Abacavir transport and metabolism;Metabolism;Transport of bile salts and organic acids, metal ions and amine compounds;SLC-mediated transmembrane transport;Transport of small molecules;Organic cation transport;Organic cation/anion/zwitterion transport;Histidine metabolism (Consensus)

Recessive Scores

• pRec: 0.173

Intolerance Scores

• loftool: 0.682
• rvis_EVS: -0.45
• rvis_percentile_EVS: 24.19

Haploinsufficiency Scores

• pHI: 0.111
• hipred: N
• hipred_score: 0.408
• ghis: 0.591

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.181

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Slc22a3
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: drug transmembrane transport;organic cation transport;quaternary ammonium group transport;regulation of appetite;histamine uptake;dopamine uptake;toxin transport
• Cellular component: plasma membrane;integral component of plasma membrane;membrane
• Molecular function: dopamine:sodium symporter activity;protein binding;organic cation transmembrane transporter activity;quaternary ammonium group transmembrane transporter activity;toxin transmembrane transporter activity